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The Research and Application of Metabolism Network and Pathway

Author: LiuRong
Tutor: LiuJunWan
School: Central South University of Forestry Science and Technology
Course: Applied Computer Technology
Keywords: Metabolism Network Bioinformatics Systems Biology Petri Nets
CLC: Q493
Type: Master's thesis
Year: 2008
Downloads: 133
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Abstract

In the post-genome era, the methods of bioinformatics research play an important role in unraveling the complex mechanisms inside biological systems. Conventional molecular biological approaches, though very useful in studying the functions of single gene or protein, could not meet the demands of understanding the dynamic interactions in the whole biological systems, such as a cell, an organ, etc. With the development of high throughput technology, accumulating tons of experiment data, it is necessary to study the structure of biology networks with systemic viewpoint. So the growth of "systems biology" is possible.Systems biology tries to understand the biological systems at the systematic level. In the field, modeling and simulation of biochemical networks are one of the most important steps. The constitution of the model is the foundation of understanding and resolving the life phenomenon systematically. Current research can be divided into two categories. They are structural analysis of the network based on graph theory, and dynamic system analysis of the network based on differential equations.Based on the Systems Biology methodology, the thesis introduces Petri Nets as its modeling metabolism tool which is prevailing in system engineering. The basic theory knowledge of Petri Net is presented, and the description of Petri Net metabolic model is denoted. Meanwhile, the analyze theory of Petri Net such as boundedness, S Invariant, T Invariant and optimization are discussed to simulate the model. These ways and means are good instruments to model and imitate. Based on the equation about biochemistry reaction of Anaerobic and Aerobic metabolic, the thesis has established their Petri Net models.At present, there have been many databases of biochemistry networks, but each one has different emphasis. After analyzing the application and research status, the origin of data and the technology of pathway database, this thesis is go on designing a pathway database with relation database technology. It makes use of SQL Server2000 as DBMS (database manage system). The data from EcoCyc database are the data source of the pathway database. On the groundwork, the thesis designs a pathway tool which firstly applied Petri nets as the relational model successfully. It can present the relational information and pathway of mode biology E.Coli neatly and conveniently.

The Research and Application of Metabolism Network and Pathway

Abstract

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